Red and Blue
by TRikiD
Summary: Sonic is shocked to discover that Doctor Eggman was able to use his own special DNA and create a powerful hedgehog to battle him. But when the mutant hedgehog becomes free of Eggman's control, Sonic learns that they are more connected than they thought, and that they need each other to survive.
1. Chapter 1 - What If?

Red and Blue

Chapter 1 - What If?

Just outside of our planet, Earth, a large and alien spaceship of the evil Doctor Eggman, hovered amongst the darkness and stars as he skulked and schemed.

To launch his flawless plan, he had captured Miles 'Tails' Prowess to lure the world's fastest hedgehog and force him to use the Chaos Emeralds to rescue his beloved fox friend.

If there was one thing Sonic knew, it's that _no one_ messed with his friends, or anyone innocent for that matter, and he would do anything to protect them.

As the hedgehog approached Eggman's ship, his golden fur and red eyes continued to glow brighter from the power of the Emeralds. Bracing for impact, Sonic crashed head first through an docking station and headed straight for the cockpit of Eggman's ship.

But if Sonic knew Eggman, he knew there would be a trap waiting for him.

But upon the cockpit, the room was surprisingly quiet. Too quiet for Sonic's liking, not to mention that Eggman was nowhere in sight. On the other side of the room, Tails was unconscious and rendered immobile with chains. But it's what he was chained to that was the problem; the two-tailed fox was chained to a giant red laser gun that took up a quarter of the room, but there was something off about the obvious world-dominating weapon.

For one thing, even though it was more or less pointed down to Earth, it didn't seem to be active. And two, there was no one at the laser's control panel; not even Eggman was there to give an evil yet cliché speech.

But Sonic wasn't going to risk losing the chance of rescuing Tails, so he rushed to his unconscious friend, and used a spin dash to cut through both chains with ease.

"Tails! Tails, you ok, Buddy?" Sonic whispered urgently, but Tails wouldn't move or make a sound.

"Geez, Eggman…what did ya do to him?" Sonic grunted as he lifted the fox up and draped him over his shoulders, failing to notice how much heavier he had become.

"Only what was necessary!" Sonic looked up to find Eggman and his two robot minions, Orbot and Cubot, entering the room, and the evil egg-shaped doctor was wearing a satisfied grin.

"Hey, Eggy! Long time, no see! I was afraid you've run out of evil plans for old time's sake," Sonic mocked.

"No, Hedgehog, I haven't given up—I've just been away, creating a foolproof plan, that will _surely_ defeat you so that I can conquer the world. And this time, I think you'll want to sit down, because I've got a pretty interesting scheme," Doctor Eggman chuckled darkly.

"I don't have to listen to anything you have to say, Eggman! I've got what I came for!"

"Oh, but on the contraire, Sonic—I believe it is your 'friend' who has you!"

With that, Tails suddenly jolted to life, but the mechanical whirring and glowing red eyes immediately told Sonic it wasn't his friend, but a robot replica.

Sonic threw the robot as hard as he, but robot Tails proved to be much too fast for sonic, as it grabbed his back quills in a vice grip; the force of Sonic's throw caused the robot to tear a few big clutches of quills from his back.

The hedgehog screamed in pain as he collapsed to his knees, the power of the Chaos Emeralds nearly fading from his body when he nearly lost too much focus. But Sonic wasn't going to give up just yet.

"You're going to have to rip out more than that ta defeat me, Doc," Sonic grunted in pain as he slowly stood back up, but that's when he was greeted with the sight of the real Tails, who was fully awake, bounded and gagged, as Orbot and Cubot brought carried him.

"Then how about after we rip out this little tod's heart instead?" Eggman taunted, reaching a claw-like hand out to Tails.

"Erm…technically, you would need surgical equipment to perform such a thing. Without the proper equipment, it would cause long and sufferable pain for Tails," Orbot couldn't help but inform.

"That's the point, you dope!" Cubot snapped, and Eggman sighed and slapped a hand to his forehead in disappointment.

"Nevermind! The point now is, I finally have what I need," Doctor Eggman interrupted, and he smiled at robot Tails, as it handed him all of Sonic's quills he had managed to fatally pluck, blood dripping off a few of the nerve ends, and they faded back to his normal blue hue after they were disconnected from the power of the Chaos Emeralds.

"What're you gonna do with a few petty quills?" Sonic inquired meekly.

"Oh, haven't you heard? You're Sonic the Hedgehog, the world's only high-speed hedgehog. You're quite special, Sonic. And not only that, but you also have the ability to master the Chaos Emeralds' ancient powers—but let's face it, with all that power, we're practically playing an unfair game of Hero and Villain—so that's when I figured I should level out the playing field."

"What are you talking about?"

"Are you blunt?" Orbot cut in flatly.

"Yeah, can't'cha tell he's goin' ta cheat?" Cubot growled.

"ENOUGH!" Everyone froze at the sound of Doctor Eggman's booming voice. "With these quills, I can take the rather useful DNA samples from them, and _your_ samples will be the last ingredient to my little project."

"Which is…?" Sonic hissed.

"I can assure you, it will be my second greatest achievement," Eggman informed with a wicked grin. Before Eggman went on, he walked up to the ship's control panel, and pulled down on a large lever.

The result of the lever being pulled was a hole in the floor opening in the middle of the room, and a large vat filled with bright green bubbling liquid slowly arose from the darkness, bubbling liquid; sitting inside the sealed vat was a large red sphere, occasionally molting like the material you would find in a lava lamp.

"What is that?" Sonic asked in awe, not taking his eyes off the orb.

"You know, they don't call me 'Doctor' for nothing. Just because I never finished medical school, doesn't mean I'm not a good physicist. I used all of my experience to create this little beauty," Eggman began as he walked up to the vat and pressed a hand to the glass, "And just wait until you see it in action—it'll finally be enough to take you down, Hedgehog. All it needs is an original DNA strand of your, and it will be complete."

"What do you mean? What are you going to do with them?"

"I'm simply going to input your DNA into it. Once that happens, you will no longer be the world's fastest hedgehog—and it will be the greatest and only weapon I ever needed."

"Only weapon? Then explain _that_?" Eggman cocked an eyebrow and followed Sonic's finger, which was pointed at the large ray gun.

"That's simply part two of my plan. My Red Runner here is going to help launch it."

"Red Runner?" Sonic repeated under his breath, and he then realized he must have been referring to whatever was trapped in the vat, "You can't do this, Eggman!"

"And why not?"

"Because you've never won before. What makes you think you even stand a chance now?"

"There's a first time for everything, Sonic—and I believe my first victory is nigh."

Eggman began to laugh evilly at that, and he handed the quills back to robot Tails, who flew up to the top of the vat and dropped the quills into it like he were feeding a fish.

"NO!"

Just as the quills slowly sank closer to the red orb, Sonic suddenly performed another spin dash, but Eggman and his robotic minions moved out of the way just in time, causing him to hit the only thing that couldn't dodge him: The vat. The glass container shattered upon impact, and green liquid spilled everywhere, along with the red orb that splat like egg yolk on the floor.

"No, my probject!" Eggman cried and ran up to the red goop. But as he sulked over his lost project, Sonic was busy freeing Tails from Orbot and Cubot and undid his bindings.

"Phew! Thanks, Sonic!" Tails cheered.

"Don't thank me yet! First, we gotta get outta here! See ya, Eggy!" Sonic shouted and grabbed Tails' hand, and the said young fox propelled his two tails, as the two flew out of the ship to head back home.

"This isn't fair! I was so close! I knew I should've thought of a better trap for that hedgehog! I could've finally destroyed him and taken over the world, and then the universe!" Eggman rambled on angrily, getting down on his knees and banging his fists on the ground.

"Well, maybe you can try again, Sir?" Orbot guessed, but Eggman never said anything. The robots sat there in silence, waiting for their boss to say something or even move. But he just sat there, leaning over his destroyed work.

"No."

"What?" Orbot and Cubot questioned.

"No, I don't need to try again," Eggman repeated firmly, "I didn't fail. Look."

Cubot, Orbot, and robot Tails looked at the red goop at Eggman's knees, and they noticed that Sonic's quills had stuck out like sticks in the mud, but then they noticed something else; the goop was starting to move and twitch in the places where the quills punctured it.

"It's still alive!" Eggman stated with excitement, scrambling to place any other misplaced quills into his project. Once he had gathered the rest, he sprinkled them all over the red puddle. And then they waited.

And just as Eggman predicted, to the touch of the rest of the quills, the red goop started to have a much stronger reaction; it began to twitch violently, and before long, it consumed each quill.

"What's it doing?" Cubot asked as he and the other robots backed away in fright, but Eggman stood with pride, as the goop quickly rose from the floor and took a familiar form.

Though it was quite unexpected, Eggman still grinned at how his project had turned out, especially when it took the form of hedgehog.

"Greetings, Red Runner," Eggman greeted softly, as the red hedgehog stumbled onto its hands and knees in exhaustion.

"You three, hurry up! Input the nerve transmission chip!"

The three robots quickly grabbed the mutant and held it with a vice grip, and just being 'born', it was still pretty week and couldn't defend itself. Soon, Cubot pulled out small gun with a large spike on the end, almost like a stapler.

"Hold still! This isn't going to hurt—me!" Cubot cackled and suddenly stabbed the hedgehog in the back of its neck with the spike, not hesitating pulling the trigger. The red hedgehog grunted and screamed in pain, as the chip was pushed deep into its neck.

* * *

Sonic grunted when he felt a faint stinging pain in the back of his neck and down his spine; he started to message the pain away, as he recalled that he and Tails stopped by a hot dog cart in New York.

"You ok, Sonic?" Tails asked with concern, walking back from the cart with a chili dog and a regular hot dog with ketchup, and handed the chili dog to the said blue hedgehog.

"W-What do you mean?" Sonic denied

"I mean, you were totally spacing out, and you look a little pale."

"Right…well…" Sonic tried to search for the right words, but he stalled by shoving the chili dog in his mouth, "I don't know…maybe it was just some arthritis?"

"How? You _never_ get arthritis."

"Arthritis or not, it's nothing a little aspirin can't cure."

"Well, if ya say so…"

But just as the two tried to let it go, Sonic couldn't help but let his mind take him somewhere else again, as Tails just walked on without him. Sonic felt more pain in his neck and back, albeit faint, while staring up at the clear blue sky.

 _What if Eggman_ _was_ _right?_ Sonic pondered.

* * *

 **T** **his is my first Sonic the Hedgehog fanfic, so please don't be mean!**

 **Until the next chapter, I'm TRikiD, bye-bye!**


	2. Chapter 2 - Red Runner

Chapter 2 - Red Runner

After stopping yet another one of Eggman's scheme's nearly two weeks ago, Sonic and Tails hung around New York for a bit and even stayed at a rather nice hotel, to which Sonic took advantage of the luxurious beds for his abnormal sleeping habits.

One night, he headed back their room alone, as Tails was still out doing whatever. Sonic yawned and plopped down onto his bed, too tired to watch TV; he didn't even bother to check on the Chaos Emeralds, which were lazily stuffed into a satchel on an armchair.

He just turned over without pulling over the covers or taking his shoes off; the pale light of the full moon shining through the window, and went right to sleep.

Unfortunately, being a heavy sleeper, Sonic failed to notice the conspicuous shadowy figure that lowered itself over the window with a rope and safety harness. Sonic and Tails' room was on the fifth floor, meaning one slip and he would fall many stories, likely to his death.

It was hard to remain stationary with the wind blowing through his black trench coat, causing him to swing a bit. But soon enough, he pulled out a razor and performed another cliché spy move by smoothly and soundlessly cutting a perfect circle in the window.

When the circle was completely cut, it suddenly leaned in, and it would've shattered and woke Sonic up if the shadowy figure hadn't caught the glass circle just in time; he then pulled it out and tossed it, not caring about who or what it would hit on the way down.

The shadow unclipped his vest and jumped in without a sound, and Sonic only snorted in response. The shadow stood up straight and rolled his eyes at the sight of the arrogant blue hedgehog, and that's when the glimmer of the Chaos Emeralds caught his eye.

The stranger threw the satchel strap over his shoulder, and secured the Emeralds inside by shutting the satchel tight. But the intruder's luck ran out when the door opened, and Tails walked in, immediately screaming when he turned on the lights and finally noticed the stranger.

"AHH! THEIF!" Tails' screams woke Sonic with a fright, but he was even more surprised to find a red hedgehog, dressed in a leather black trench coat, and wearing a mask Teenage Mutant Ninja Turtle style, with the Chaos Emeralds in his grasp.

Before Sonic could even get off of the bed, the thief jumped back out the window and secured the rope, blowing a raspberry at Sonic before falling straight down.

Sonic wasn't going to give up that easily, though; without even thinking, he jumped out the window, too, plummeting towards the descending thief.

"Give those back!"

The stranger only looked at Sonic with a cocked brow, and he once again rolled his eyes at him before grabbing out a grappling hook gun, unhooking from the rope again before shooting the grappling hook at the corner of another building across the street. But just before he could swing away, Sonic grabbed the satchel and clung to it for dear life.

The two hedgehogs were now swinging around the corner of a building, the thief holding the grappling gun with one hand and satchel strap in the other; Sonic refused to let go, no matter how hard the red hedgehog tried to shake him off.

With Sonic's added weight, the thief wasn't able to focus on pulling himself up, and the two were sent swinging to a lower floor of the hotel, crashing through a window and landing in the gym.

The satchel flap flipped opened, and the seven Chaos Emeralds all spilled out. After the thief stood up and rubbed his head out of pain, he wiped off any little shards of glass, but was utterly shocked to find that the Emeralds had shattered.

The Chaos Emeralds are indestructible object of power, so a single fall would never break them. He glared at Sonic, who was chuckling as he picked himself up, holding his left arm from the pain.

"What? You thought I'd be stupid enough to take the Chaos Emeralds with me? I knew Eggman would be stupid enough ta come ta me for 'em, but you, too?" Sonic boasted, staring back into the thief's bright green eyes with confidence.

Luckily, the gym was closed hours ago, so no one around to get caught up in the line of fire; not even Sonic and the red hedgehog was fatally injured, just a few scratches and bruises.

"So, what do ya say? How about a good old fashioned bash, _Buddy_?" Sonic taunted and stood in a fighting stance, ignoring the pain in his arm, readying himself for anything…almost anything.

The red hedgehog, fast as lightning, ran up to Sonic and kicked him between his legs _hard_. Sonic screamed like little girl, collapsing to his knees and grabbing his crotch in pain.

Sonic slowly glanced up to see the thief turn and leave towards the exit, as he grabbed the satchel and dumped out the fake Chaos Emeralds, swinging the empty satchel over his shoulder to begin his search for the real emeralds.

But even though he didn't get away with the real Chaos Emeralds, Sonic wasn't going to let this pain in the neck get away that easily. But with all the pain in his groin, he could barely move. He frantically looked around for anything for anything, anything that could be used as a weapon. And then he found it.

He grabbed a fifteen pound dumbbell from the shelf, throwing it with all his hoped for the best. Next thing he knew, there was a loud thud and a grunt of pain. Bull's-eye.

Sonic was finally able to withstand the pain and get back up again, still holding his crotch, and the thief was stomping and holding his head with both hands in agony. He then pulled his hands away to check for blood, but there luckily wasn't any. The red hedgehog then gave Sonic the death glare, and he pulled his mask down around his neck.

"You hit me in the head with a DUMBBELL?!" When the thief finally spoke and removed his mask, he revealed a shocking feat: He was actually a she.

"You're a _girl_?!" Sonic gasped with just as much shock.

But he suddenly felt an aching pain in the back of his head, too, and grunted loudly while gripping his throbbing skull.

"You're pathetic, Sonic. Can't admit that you were beaten by a girl, so ya try ta bash her skull in? What is wrong with you?" the she-hedgehog growled, and Sonic's eyes widened when he heard her say his name.

"How do you know my name?"

"Why wouldn't I know the name of my sworn enemy?"

"What do you mean…wait…"

Sonic examined the red hedgehog closely, finally realizing how familiar she looked. He then recalled rescuing Tails from Eggman, and that red orb in the vat was burned into his memories. And then it hit him.

"You. You're the mutation Eggman created from my DNA… _you're_ Red Runner!"

"Ding, ding, ding! We have a winner!" Red Dash cheered sarcastically, as she clapped slowly.

"What's Eggman planning?! Tell me! And what does he need _you_ for?!" Sonic demanded.

"Isn't it obvious? I'm your doppelganger, Sonic, meaning anything you can do, I can do it, too. Except, I'm meant to do it all better, and you'll be gone once and for all."

"Ugh, you sound just like Eggman."

"I can't help it. The fat man created me!" Red Dash sounded like she was trying to tell a joke, and Sonic couldn't help but smirk. But out of nowhere, Red Runner suddenly broke down in a fidgeting mess, her quills charring from a bright light.

And as he tried to figure out what was happening, Sonic suddenly felt like her was being shocked in back of his neck as well, as if someone had stabbed him with a cattle taser. He soon collapsed in pain and paralysis, but unlike the red hedgehog, he powered through the agony and remained conscious.

"Sonic!" Tails exclaimed after the prods retracted back into his taser gun, and he rushed to the blue hedgehog's aid, "What happened?"

"If you're talkin' about the electric wave that just hit, I have no clue," Sonic meekly replied, "But I _do_ know that we've met Eggman's little protégé."

* * *

Sonic and tails apologized to the hotel manger for the damage they caused, but miraculously got away with it due to Sonic's heroic reputation; after that, they didn't hesitate to bring the female hedgehog back to their room, making sure to tie her to the armchair tightly.

"Wow, I guess Eggman's a better doctor that he let on," Tails admitted in awe, as he examined the unconscious red hedgehog, "What I don't get is this strange connection between you two. You said you felt it when I shocked her, right?"

"Yeah. But each time she hurt me, she was totally unphased—it's a little unfair, if ya ask me," Sonic grumbled while crossing his arms.

"Well, what should we do now?"

"I say we keep her close by, try to get some information on Eggman's plan outta her."

"Sorry to burst your bubble, but this bird isn't gonna sing for you," Red Runner groggily informed after finally coming to, and she wore a confident smirk on her face.

"You say that now, but you'd be surprised to find just how persuasive I can be, Sister," Sonic joked with a wink and a thumbs up, making the female hedgehog scoff.

And then she growled, her words rolling off of her tongue like poison, "I _despise_ being related to you."

"And vice versa, but that doesn't mean we can't help each other."

"And why would I help you?"

"Listen, he may be your 'dad' or whatever, but Eggman's a pretty horrible guy," Sonic began with air quotes.

"Definitely not a family man," Tails added dryly and shook his head.

"So, if you help us stop him, you won't have ta listen ta him, and you can be a free hedgehog. Deal?"

Sonic held out a hand to seal the deal, but the she-hedgehog only gave him a deadpan look, "My hands are kinda tied up. And even if they weren't, I still wouldn't indulge this stupid-GAH!"

All of a sudden, Red Runner's back arched and she threw her head back, her teeth were clenched and her hands balled into tight fists. She tried to move to make the pain go away, but her arms and legs could only fidget within their bindings.

"What's happening?" Tails questioned in fear, as both he and Sonic stepped back.

"My…chip…is short-circuiting…" she hissed through clenched teeth, "P-Please…you have to…get it out…"

"Where is it?" Sonic inquired.

"My…neck…UGH!"

Tails quickly approached to examine her neck, and he found a stitched up scar running down the back of it.

"How do we get it out?" Tails asked.

She was silent for a moment, a secret grin forming on her face as she leaned forward, "You can't."

In the blink of an eye, Red Runner reared her head back and bashed it into Tail's, nearly knocking him out. After leaning her head back, her quills cut through the bed linens that held her, and she went to work on freeing her ankles.

"You lied!" Sonic snapped, preparing for another fight.

"Sure I did. I'm a bad girl," Red Runner simply shrugged, "Au revoir!"

With that, she jumped and curled into a tight ball, glowing as she performed a Spin Dash and attacked Sonic, sending him flying back onto the bed. After ricocheting off of him, she flew out of the hole she cut in the window after grabbing her belongings.

Dazed and confused, Sonic stumbled off the bed and watched as she used her grappling hook to swing from building to building again.

"I ain't done with you yet, Sister," Sonic snarled and got a running start, jumping out of the window and breaking his fall by landing on a bounce pad below.

Be flew all the way up to the roof of another building, and set chase to Red Runner by jumping from rooftop to rooftop. His running proved to be faster than her swinging, but Red Runner wasn't going to let him get too close. At the trough of her swing, she kicked her legs up and pulled the hook back, landing on roof a few buildings ahead of Sonic.

She started sprinting at unimaginable speeds, taking Sonic by surprise; although, he knew he couldn't let this get to him, and picked up speed as well.

Unlike Red Runner, Sonic collected a few golden rings lined up on the roofs, quickly gaining more speed than her. Sonic went off and made a large turn, curling around until he met up with her in mid-jump between buildings.

The red hedgehog never expected it, and she was helplessly caught in the line of Sonic's spin dash; intense pain coursed through both hedgehog's ribs, and Red Runner swore she heard one snap upon impact.

Despite a rib breaking for Red Runner, Sonic only felt like the wind was knocked out of him. But now, both hedgehogs were plummeting, the busy streets of New York growing closer and closer. But maybe being the righteous hero he is, or not wanting to risk feeling her deadly landing, or maybe a combination of both, Sonic desperately reached out to Red Runner and held her close before landing on yet another bounce pad on the side of a building.

He held the meek red hedgehog bridal style as he bounced up to another rooftop, landing safely and gently putting her back down.

"You…didn't need…to do that," Red Runner grunted as she hunched over, holding an arm against her aching chest.

"Sorry, Sis, but you know what they say," Sonic protested while wagging a finger, "Twins can feel each other's pain."

* * *

 **These two sure do have a strange connection. Maybe it'll come back to bite them?**

 **Until the next chapter, I'm TRikiD, bye-bye!**


End file.
